As congestion worsens, the importance of rigorous methodologies to estimate travel time reliability increases. Exploiting fine-granularity transit GPS data, this research proposes a novel method to estimate travel time percentiles and confidence intervals. Novel transit reliability measures based on travel time percentiles are proposed to identify and rank low-performance hot spots; the proposed reliability measures can be utilized to distinguish peak-hour low performance from whole-day low performance. As a case study, the methodology is applied to a bus transit corridor in Portland, Oregon. Time–space speed profiles, heat maps, and visualizations are employed to highlight sections and intersections with high travel time variability and low transit performance. Segment and intersection travel time reliability are contrasted against analytical delay formulas at intersections—with positive results. If bus stop delays are removed, this methodology can also be applied to estimate regular traffic travel time variability.